Re: puzzle of SMD in NAMD-2.9 and pull code in Gromacs

From: Axel Kohlmeyer (
Date: Tue Dec 10 2013 - 08:22:18 CST

On Tue, Dec 10, 2013 at 1:02 PM, dbaogen <> wrote:
> Dear all,
> Recently, I have a problem in using SMD to pull a ligand out
> from the protein active site. In the course of pulling, the protein is
> moving along with ligand. So the results are not consistent with our
> expectation. If we impose the harmonic restraint on protein, the ligand can
> be pulled out. But the artificial effect would be introduced if we did it
> like that. Would anyone like to give me some suggestions about the SMD
> simulation in NAMD?
> In addition, it is found that the pull code in Gromacs can also do
> the SMD simulation. From the published results using pull code in Gromacs,
> the protein itself was not restricted while pulling a ligand out from the
> protien's active site. Would you like to explain the difference between SMD
> in NAMD and pull code in Gromacs? Thanks in advance!

well, first *you* have to explain what were the differences in the
*rest* of the simulation. did you employ the exact same force field,
for example?


> Best
> Duan Baogen

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.

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